My Max has also been battling an URI. It started with pretty severe bronchitis, which, thanks to the nebulizer, we've cleared up.
Like you, my vet prescribed baytril first to see if that worked. It didn't. Sas had posted nebulizing info in the resource center, so I emailed that to my vet. He didn't have a nebulizer on hand, so I rented one from a local pharmacy for $10 a week until the one I bought on ebay (for 30.00) arrived.
We still kept up with the baytril, but I also nebulized him for 15 min2x a day. We used a cocktail of sterile saline (3ml) and mucomyst(.3ml).
Also, because a lot of Max's problems were also nasal, we used gentamycindrops in his nose 2x a day.
This worked like a charm. Unfortunately, he still has nasal problems right now, but the bronchitis completely cleared up.
Oh, and for the nebulizing chamber, I made one myself out of a large tupperware box. See the links in the resource center for more info.
Respiratory Infections
I'll be praying for your little one. These URI's can be pretty resilient.